Qualitative Description for Assembly and Annotation of Transcriptomes
We assembled and compared genome-wide transcription profiles of ESM and ASM virgin adult females and females after mating and oviposition. Eight independent RNA-Seq analyses were performed with different populations.
A total of 205.96Gb of processed reads were obtained by sequencing (>6.98 Gb/replicate). The percentage of Q30-filtered bases was more than 91.85%. Assembly of the sequence data from all libraries resulted in identification of 129,286 unigenes (Table 1).
Table 1
Transcriptome assembly results for all samples
Type
|
Result
|
Total transcripts (filtered)
|
176,654
|
Total unigenes
|
129,286
|
Total sequence, bases
|
120,861,580
|
Unigene/transcript average length
|
684.17
|
E90N50
|
2,400
|
GC percent
|
39.13
|
Mean mapped reads
|
3737.048531
|
TransRate score
|
0.15799
|
BUSCO score
|
C:96.8% [S:86.2%;D:10.6%]
|
The length distribution of the unigenes is shown in Figure 1. The percentage of unigenes with a length not greater than 500 bp was over 70%, with a further 17% ranging between 501 and 1000 bp. Relatively few unigenes were found in the 4001-4500 bp category.
All female adult transcriptome unigenes were annotated from the NR,Swiss-Prot, Pfam, COG, GO and KEGG databases. The number of unigene annotations was 39,584, accounting for 30.62% of the total. Among them, queries of the NR database yielded the most annotations, accounting for 26.28% of the total. The COG database yielded the least annotations, 6,221 (4.81%) (Table 2).
Table 2
Unigenes annotation profiles of all spongy moth samples
Database
|
Unigene number (proportion)
|
NR
|
33,971 (0.2628)
|
Swiss-Prot
|
27,450 (0.2123)
|
Pfam
|
24,831 (0.1921)
|
COG
|
6,221 (0.0481)
|
GO
|
22,408 (0.1733)
|
KEGG
|
21,260 (0.1644)
|
Total annotated
|
39,584 (0.3062)
|
Total
|
129,286 (1)
|
Note: Total annotated = number of unigenes annotated in one or more databases.
NR annotation
BLASTX comparison with NR database sequences was performed to identify the similarity between the transcription sequences of spongy moth and similar species and the functional information of homologous sequences. A total of 33,971 unigenes were successfully matched with known genes (E<10-5), with 4,716 (14.03%) sequences showing high sequence similarity with Spodoptera litura, followed by Helicoverpa armigera, There were 4,467 (13.29%) and 3,666 (10.91%) unigenes with top BLAST matches with Heliothis virescens sequences. Matches with other species returned by BLAST showed low sequence similarity with spongy moth sequences. However, 11,927 unigenes (35.49%) were unique transcripts of spongy moth (Figure 2).
COG/NOG annotations
COG (Clusters of Orthologous Groups) is a database of protein lineages for general function prediction, while NOG (Non-Supervised Orthologous Groups) is optimized on the basis of COG to expand genomic information and provide more detailed OG analysis. After comparison, COG function classification of genes/transcripts can be obtained. The most prevalent COG functions annotated in the transcriptomes of adult spongy moth are translation, ribosomal structure and biogenesis, while the Function unknown class was the most prevalent annotation in NOG (Fig 3).
GO annotation
A total of 22,408 Unigene sequences were annotated with 94,399 GO entries, including 48 subclasses in 3 categories: 20 biological_processes subclasses, 14 cell_components subclasses, and 14 molecular_functions subclasses. The largest number of annotations were for biological process (37,112; 39.3%), and the least was molecular_function (26,424; 28%) (Figure 4).
KEGG pathway
Biological functions of transcripts in the spongy moth transcriptomes were identified with the assistance of KEGG (Kyoto Encyclopedia of Genes and Genomes), a large knowledge base for analyzing gene functions and linking genomic information with functional information. We found that there was a total of 21,260 unigenes that mapped to six pathways, including Metabolism, Genetic Information Processing, Environmental Information Processing, Cellular Processes, Organismal Systems, and Human Diseases. Among them, the most unigenes (3,118) mapped to the Signal Transduction subgroup under Environmental Information Processing (Figure 5).
Strain-specific differences in gene expression
A total of 6,692 unigenes were found to be differentially expressed in pairwise comparisons of ASM and ESM transcriptomes, including 5,371 up-regulated and 1,321 down-regulated DEGs in ASM relative to ESM (Supplementary Table 1). Approximately two orders of magnitude more differentially-expressed genes (DEGs) were observed in pairwise comparisons of ASM and ESM transcriptomes (JGS vs. CT, JGS vs. NJ, ZY vs. CT, ZY vs. NJ) relative to the number of DEGs found with pairwise comparisons of transcriptomes from the same biotype (JGS vs. ZY, CT vs. NJ). The number of the DEGs are shown in Table 3.
Table 3
The number of up-regulated and down-regulated DEGs between four geographic spongy moth strains.
Groups
|
Up-regulated1
|
Down-regulated1
|
JGS_ZY
|
108
|
53
|
CT_NJ
|
19
|
11
|
JGS_CT
|
3434
|
757
|
JGS_NJ
|
3027
|
592
|
ZY_CT
|
3201
|
888
|
ZY_NJ
|
2995
|
708
|
1Numbers refer to the quantity of up- or down-regulated DEGs in the first strain listed in each pairwise comparison relative to the second strain.
In four pairwise comparisons of ASM transcriptomes with ESM transcriptomes (e.g., JGS vs CT, JGS vs NJ, ZY vs CT, and ZY vs NJ), 306 DEGs consistently exhibited up-regulation and 2,309 DEGs consistently exhibited down-regulation in ASM transcriptomes relative to ESM transcriptomes showed in Supplementary Table 2. Table 4 lists the 40 DEGs with the greatest degree of up- or down-regulation in ASM-ESM pairwise comparisons. The 20 DEGs with the greatest degree of down-regulation in ASM relative to ESM included cytochrome c oxidase (COX) subunits I, Ⅱ& Ⅲ; cytochrome b oxidase; NADH dehydrogenase subunits 1&4; ATP synthase subunit 6; glucose dehydrogenase; myelin protein P0 isoform L-MPZ precursor; myelin basic protein isoform X3; myosin-4; and moricin. Among the 20 DEGs up-regulated to the greatest extent in ASM transcriptomes were pancreatic triacylglycerol lipase-like, alkaline C trypsin, calphotin-like, serine protease 1-like, non-specific lipid-transfer protein, L-serine dehydratase/L-threonine deaminase, trypsin precursor AiT6, actin cytoskeleton-regulatory complex protein PAN1-like, NADH dehydrogenase subunit 1, vitellogenin 7 precursor, vitellogenin 2 isoform 1 precursor, and chitin deacetylase 1&8.
Table 4
Genes that were consistently differentially expressed in all comparisons in four ASM and ESM transcriptomes. DEGs are sorted in descending order with respect to log2-fold change, with down-regulated DEGs listed first, followed by up-regulated DEGs.
Gene ID
|
Comparison
|
log2FoldChange
|
Adj-P25
|
Gene expression level (GEL)
|
NR hits
|
CN_JGS
|
CN_ZY
|
USA_CT
|
USA_NJ
|
TRINITY_DN56697_c1_g2
|
ZY_NJ
|
-34.83374762
|
2.86E-56
|
-
|
0
|
-
|
67.14
|
none
|
ZY_CT
|
-34.35069549
|
1.55E-54
|
-
|
0
|
70.09
|
-
|
JGS_NJ
|
-24.73745878
|
4.62E-27
|
0
|
-
|
-
|
67.14
|
JGS_CT
|
-24.25440666
|
5.39E-26
|
0
|
-
|
70.09
|
-
|
TRINITY_DN13504_c0_g1
|
ZY_NJ
|
-34.17627032
|
9.52E-50
|
-
|
0
|
-
|
79
|
none
|
ZY_CT
|
-34.26177166
|
5.12E-50
|
-
|
0
|
89.51
|
-
|
JGS_NJ
|
-24.49561347
|
1.83E-24
|
0
|
-
|
-
|
79
|
JGS_CT
|
-24.58111481
|
1.14E-24
|
0
|
-
|
89.51
|
-
|
TRINITY_DN58366_c8_g2
|
ZY_NJ
|
-27.45125641
|
2.58E-08
|
-
|
0
|
-
|
0.37
|
XP_028035360.1 gloverin 4
|
ZY_CT
|
-33.80514904
|
8.43E-13
|
-
|
0
|
21.88
|
-
|
JGS_NJ
|
-16.36806188
|
0.005321
|
0
|
-
|
-
|
0.37
|
JGS_CT
|
-22.7219545
|
8.32E-06
|
0
|
-
|
21.88
|
-
|
TRINITY_DN33204_c1_g1
|
ZY_NJ
|
-27.85583552
|
1.27E-08
|
-
|
0
|
-
|
57.34
|
none
|
ZY_CT
|
-29.99664328
|
4.52E-10
|
-
|
0
|
90.23
|
-
|
JGS_NJ
|
-18.12384237
|
0.001125
|
0
|
-
|
-
|
57.34
|
JGS_CT
|
-20.26465013
|
0.000121
|
0
|
-
|
90.23
|
-
|
TRINITY_DN72186_c0_g1
|
ZY_NJ
|
-25.36839952
|
4.25E-10
|
-
|
0
|
-
|
2.65
|
AKJ54509.1 moricin
|
ZY_CT
|
-31.15021215
|
1.26E-15
|
-
|
0
|
63.53
|
-
|
JGS_NJ
|
-16.27525422
|
0.000381
|
0
|
-
|
-
|
2.65
|
JGS_CT
|
-22.05706685
|
8.5E-08
|
0
|
-
|
63.53
|
-
|
TRINITY_DN83020_c0_g1
|
ZY_NJ
|
-27.25754436
|
8.35E-10
|
-
|
0
|
-
|
5.9
|
none
|
ZY_CT
|
-26.94823185
|
1.28E-09
|
-
|
0
|
2.84
|
-
|
JGS_NJ
|
-21.67189109
|
3.4E-06
|
0
|
-
|
-
|
5.9
|
JGS_CT
|
-21.36257859
|
4.68E-06
|
0
|
-
|
2.84
|
-
|
TRINITY_DN61670_c0_g1
|
ZY_NJ
|
-25.33900066
|
4.94E-07
|
-
|
0
|
-
|
0.21
|
none
|
ZY_CT
|
-31.4905229
|
4.2E-11
|
-
|
0
|
20.97
|
-
|
JGS_NJ
|
-15.54852005
|
0.010722
|
0
|
-
|
-
|
0.21
|
JGS_CT
|
-21.7000423
|
2.65E-05
|
0
|
-
|
20.97
|
-
|
TRINITY_DN23060_c0_g1
|
ZY_NJ
|
-26.72574954
|
6.03E-10
|
-
|
0
|
-
|
3.73
|
XP_026735683.1 glucose dehydrogenase [FAD, quinone]-like
|
ZY_CT
|
-26.19938465
|
1.36E-09
|
-
|
0
|
2.52
|
-
|
JGS_NJ
|
-21.551178
|
1.85E-06
|
0
|
-
|
-
|
3.73
|
JGS_CT
|
-21.02481311
|
3.5E-06
|
0
|
-
|
2.52
|
-
|
TRINITY_DN38260_c0_g1
|
ZY_NJ
|
-9.16728883
|
2.38E-15
|
-
|
0
|
-
|
18.88
|
ABG11762.1 cytochrome b
|
ZY_CT
|
-8.727985703
|
8.95E-14
|
-
|
0
|
15.11
|
-
|
JGS_NJ
|
-9.427663179
|
2.68E-16
|
0
|
-
|
-
|
18.88
|
JGS_CT
|
-8.988360052
|
1.12E-14
|
0
|
-
|
15.11
|
-
|
TRINITY_DN42442_c0_g1
|
ZY_NJ
|
-9.226958661
|
8.6E-16
|
-
|
0
|
-
|
7.15
|
ABV22517.1 NADH dehydrogenase subunit 4
|
ZY_CT
|
-8.750104651
|
4.76E-14
|
-
|
0
|
5.17
|
-
|
JGS_NJ
|
-9.487333085
|
9.01E-17
|
0
|
-
|
-
|
7.15
|
JGS_CT
|
-9.010479076
|
5.73E-15
|
0
|
-
|
5.17
|
-
|
TRINITY_DN55289_c1_g2
|
ZY_NJ
|
-9.300640442
|
6.44E-16
|
-
|
0
|
-
|
3.69
|
YP_004111298.1 cytochrome c oxidase subunit I
|
ZY_CT
|
-8.762913375
|
5.83E-14
|
-
|
0
|
2.64
|
-
|
JGS_NJ
|
-9.561014708
|
6.9E-17
|
0
|
-
|
-
|
3.69
|
JGS_CT
|
-9.023287641
|
7.15E-15
|
0
|
-
|
2.64
|
-
|
TRINITY_DN45473_c0_g2
|
ZY_NJ
|
-9.265572917
|
3.12E-16
|
-
|
0
|
-
|
30.97
|
YP_009024856.1 cytochrome c oxidase subunit II
|
ZY_CT
|
-8.815963642
|
1.53E-14
|
-
|
0
|
22.99
|
-
|
JGS_NJ
|
-9.525947428
|
3.29E-17
|
0
|
-
|
-
|
30.97
|
JGS_CT
|
-9.076338152
|
1.73E-15
|
0
|
-
|
22.99
|
-
|
TRINITY_DN58407_c9_g1
|
ZY_NJ
|
-8.111566982
|
0.001375
|
-
|
0
|
-
|
34.14
|
CAB3230287.1 unnamed protein product
|
ZY_CT
|
-10.14449048
|
9.24E-06
|
-
|
0
|
74.26
|
-
|
JGS_NJ
|
-8.371917541
|
0.00082
|
0
|
-
|
-
|
34.14
|
JGS_CT
|
-10.40484104
|
4.44E-06
|
0
|
-
|
74.26
|
-
|
TRINITY_DN57574_c0_g1
|
ZY_NJ
|
-9.372862201
|
3.12E-16
|
-
|
0
|
-
|
15.57
|
ACP50397.1 NADH dehydrogenase subunit 1
|
ZY_CT
|
-8.890982681
|
1.89E-14
|
-
|
0
|
12.23
|
-
|
JGS_NJ
|
-9.633236329
|
3.34E-17
|
0
|
-
|
-
|
15.57
|
JGS_CT
|
-9.151356809
|
2.23E-15
|
0
|
-
|
12.23
|
-
|
TRINITY_DN81391_c0_g1
|
ZY_NJ
|
-9.515567545
|
5.48E-17
|
-
|
0
|
-
|
7.7
|
NP_001300997.1 myelin protein P0 isoform L-MPZ precursor
|
ZY_CT
|
-8.805274946
|
2.58E-14
|
-
|
0
|
4.96
|
-
|
JGS_NJ
|
-9.775941742
|
5.36E-18
|
0
|
-
|
-
|
7.7
|
JGS_CT
|
-9.065649142
|
3.05E-15
|
0
|
-
|
4.96
|
-
|
TRINITY_DN56710_c3_g2
|
ZY_NJ
|
-9.407242996
|
3.66E-15
|
-
|
0
|
-
|
23.56
|
none
|
ZY_CT
|
-9.165370434
|
2.58E-14
|
-
|
0
|
22.13
|
-
|
JGS_NJ
|
-9.667616094
|
4.54E-16
|
0
|
-
|
-
|
23.56
|
JGS_CT
|
-9.425743532
|
3.38E-15
|
0
|
-
|
22.13
|
-
|
TRINITY_DN38334_c0_g1
|
ZY_NJ
|
-10.16900024
|
2.33E-19
|
-
|
0
|
-
|
41.75
|
AAD15020.1 cytochrome oxidase III
|
ZY_CT
|
-9.685566124
|
2.08E-17
|
-
|
0
|
31.08
|
-
|
JGS_NJ
|
-10.42937307
|
1.82E-20
|
0.17
|
-
|
-
|
41.75
|
JGS_CT
|
-9.945938954
|
1.98E-18
|
0.17
|
-
|
31.08
|
-
|
TRINITY_DN43889_c0_g1
|
ZY_NJ
|
-10.24363704
|
3.43E-20
|
-
|
0
|
-
|
37.25
|
ABG11760.1 ATP synthase F0 subunit 6
|
ZY_CT
|
-9.726532977
|
4.72E-18
|
-
|
0
|
27.24
|
-
|
JGS_NJ
|
-10.50401005
|
2.29E-21
|
0.14
|
-
|
-
|
37.25
|
JGS_CT
|
-9.98690599
|
4.23E-19
|
0.14
|
-
|
27.24
|
-
|
TRINITY_DN24402_c0_g1
|
ZY_NJ
|
-10.26592127
|
3.66E-20
|
-
|
0
|
-
|
11.26
|
XP_006255059.1 myelin basic protein isoform X3
|
ZY_CT
|
-9.868460973
|
1.73E-18
|
-
|
0
|
8.79
|
-
|
JGS_NJ
|
-10.52629408
|
2.47E-21
|
0
|
-
|
-
|
11.26
|
JGS_CT
|
-10.12883379
|
1.39E-19
|
0
|
-
|
8.79
|
-
|
TRINITY_DN58997_c0_g1
|
ZY_NJ
|
-9.162508683
|
2.23E-15
|
-
|
0
|
-
|
1.57
|
NP_062198.1 myosin-4
|
ZY_CT
|
-8.698819402
|
1.02E-13
|
-
|
0
|
1.15
|
-
|
JGS_NJ
|
-9.422883087
|
2.5E-16
|
0
|
-
|
-
|
1.57
|
JGS_CT
|
-8.959193806
|
1.29E-14
|
0
|
-
|
1.15
|
-
|
|
TRINITY_DN59309_c7_g2
|
ZY_NJ
|
11.83843455
|
5.95E-19
|
-
|
22.91
|
-
|
0
|
VDM16675.1 unnamed protein product
|
ZY_CT
|
11.95616158
|
2.34E-19
|
-
|
22.91
|
0
|
-
|
JGS_NJ
|
14.11976023
|
9.51E-28
|
113.37
|
-
|
-
|
0
|
JGS_CT
|
14.23748726
|
2.87E-28
|
113.37
|
-
|
0
|
-
|
TRINITY_DN59741_c2_g1
|
ZY_NJ
|
12.72258468
|
5.81E-34
|
-
|
41.06
|
-
|
0
|
NP_001096141.1 vitellogenin 7 precursor
|
ZY_CT
|
12.84031173
|
1.24E-34
|
-
|
41.06
|
0
|
-
|
JGS_NJ
|
12.27073794
|
4.19E-31
|
27.32
|
-
|
-
|
0
|
JGS_CT
|
12.388465
|
6.82E-32
|
27.32
|
-
|
0
|
-
|
TRINITY_DN36137_c0_g1
|
ZY_NJ
|
12.69990581
|
8.59E-27
|
-
|
10.56
|
-
|
0
|
none
|
ZY_CT
|
12.81763286
|
2.7E-27
|
-
|
10.56
|
0
|
-
|
JGS_NJ
|
12.11782678
|
3.91E-24
|
118.37
|
-
|
-
|
0
|
JGS_CT
|
12.23555382
|
1.14E-24
|
118.37
|
-
|
0
|
-
|
TRINITY_DN48344_c0_g2
|
ZY_NJ
|
10.1051722
|
3.12E-15
|
-
|
19.64
|
-
|
0
|
XP_012454349.1 PREDICTED: non-specific lipid-transfer protein
|
ZY_CT
|
10.22289924
|
1.26E-15
|
-
|
19.64
|
0
|
-
|
JGS_NJ
|
11.20217362
|
4.63E-19
|
40.95
|
-
|
-
|
0
|
JGS_CT
|
11.31990065
|
1.6E-19
|
40.95
|
-
|
0
|
-
|
TRINITY_DN55003_c0_g1
|
ZY_NJ
|
12.14483652
|
1.41E-31
|
-
|
45.21
|
-
|
0
|
XP_037298773.1 trypsin, alkaline C
|
ZY_CT
|
12.26256357
|
3.02E-32
|
-
|
45.21
|
0
|
-
|
JGS_NJ
|
11.9242181
|
3.65E-30
|
38.57
|
-
|
-
|
0
|
JGS_CT
|
12.04194515
|
6.18E-31
|
38.57
|
-
|
0
|
-
|
TRINITY_DN52890_c0_g1
|
ZY_NJ
|
12.04554237
|
5.43E-32
|
-
|
35.1
|
-
|
0
|
XP_026733233.1 pancreatic triacylglycerol lipase-like
|
ZY_CT
|
12.16326943
|
1.14E-32
|
-
|
35.1
|
0
|
-
|
JGS_NJ
|
11.83092459
|
1.43E-30
|
28.71
|
-
|
-
|
0
|
JGS_CT
|
11.94865165
|
2.3E-31
|
28.71
|
-
|
0
|
-
|
TRINITY_DN55622_c0_g1
|
ZY_NJ
|
11.88970792
|
3.8E-30
|
-
|
25.76
|
-
|
0
|
ACD37362.1 chitin deacetylase 1
|
ZY_CT
|
12.00743497
|
7.62E-31
|
-
|
25.76
|
0
|
-
|
JGS_NJ
|
11.66997913
|
7.92E-29
|
20.94
|
-
|
-
|
0
|
JGS_CT
|
11.78770619
|
1.73E-29
|
20.94
|
-
|
0
|
-
|
TRINITY_DN42377_c0_g1
|
ZY_NJ
|
11.28750003
|
3.7E-23
|
-
|
4.54
|
-
|
0
|
KAF4015244.1 hypothetical protein G4228_006027
|
ZY_CT
|
11.40522708
|
1.09E-23
|
-
|
4.54
|
0
|
-
|
JGS_NJ
|
11.55074074
|
2.75E-24
|
5.09
|
-
|
-
|
0
|
JGS_CT
|
11.66846779
|
7.82E-25
|
5.09
|
-
|
0
|
-
|
TRINITY_DN50963_c0_g2
|
ZY_NJ
|
10.48784096
|
7.27E-20
|
-
|
4.55
|
-
|
0
|
ABV70868.1 NADH dehydrogenase subunit 1
|
ZY_CT
|
10.60556801
|
2.49E-20
|
-
|
4.55
|
0.02
|
-
|
JGS_NJ
|
10.94915507
|
7.24E-22
|
5.84
|
-
|
-
|
0
|
JGS_CT
|
11.06688212
|
2.03E-22
|
5.84
|
-
|
0.02
|
-
|
TRINITY_DN57295_c1_g1
|
ZY_NJ
|
11.44001779
|
1.54E-27
|
-
|
24.35
|
-
|
0
|
XP_021183170.1 calphotin-like
|
ZY_CT
|
11.55774485
|
3.55E-28
|
-
|
24.35
|
0
|
-
|
JGS_NJ
|
11.14731591
|
5.82E-26
|
19.31
|
-
|
-
|
0
|
JGS_CT
|
11.26504296
|
1.4E-26
|
19.31
|
-
|
0
|
-
|
TRINITY_DN56232_c0_g2
|
ZY_NJ
|
11.41968572
|
6.3E-28
|
-
|
19.12
|
-
|
0
|
XP_026746126.1 serine protease 1-like
|
ZY_CT
|
11.53741278
|
1.42E-28
|
-
|
19.12
|
0
|
-
|
JGS_NJ
|
11.11378986
|
2.96E-26
|
15.33
|
-
|
-
|
0
|
JGS_CT
|
11.23151692
|
7.04E-27
|
15.33
|
-
|
0
|
-
|
TRINITY_DN50167_c0_g1
|
ZY_NJ
|
10.91821699
|
7.75E-20
|
-
|
4.7
|
-
|
0
|
NP_001069130.1 L-serine dehydratase/L-threonine deaminase
|
ZY_CT
|
11.03594403
|
2.79E-20
|
-
|
4.7
|
0
|
-
|
JGS_NJ
|
11.11276535
|
1.31E-20
|
5
|
-
|
-
|
0
|
JGS_CT
|
11.2304924
|
4.31E-21
|
5
|
-
|
0
|
-
|
TRINITY_DN59741_c3_g2
|
ZY_NJ
|
11.34624617
|
6.95E-25
|
-
|
20.09
|
-
|
0
|
NP_001038378.1 vitellogenin 2 isoform 1 precursor
|
ZY_CT
|
11.46397323
|
1.94E-25
|
-
|
20.09
|
0
|
-
|
JGS_NJ
|
10.59073727
|
2.52E-21
|
11.71
|
-
|
-
|
0
|
JGS_CT
|
10.70846432
|
7.7E-22
|
11.71
|
-
|
0
|
-
|
TRINITY_DN40081_c0_g1
|
ZY_NJ
|
11.06828843
|
1.34E-26
|
-
|
16.58
|
-
|
0
|
XP_021200296.1 pancreatic triacylglycerol lipase-like
|
ZY_CT
|
11.18601549
|
3.38E-27
|
-
|
16.58
|
0
|
-
|
JGS_NJ
|
10.86791667
|
1.85E-25
|
13.61
|
-
|
-
|
0
|
JGS_CT
|
10.98564372
|
4.61E-26
|
13.61
|
-
|
0
|
-
|
TRINITY_DN45101_c0_g1
|
ZY_NJ
|
11.02602771
|
1.13E-26
|
-
|
14.45
|
-
|
0
|
XP_014365314.2 chitin deacetylase 8
|
ZY_CT
|
11.14375477
|
2.83E-27
|
-
|
14.45
|
0
|
-
|
JGS_NJ
|
10.71648951
|
5.86E-25
|
11.31
|
-
|
-
|
0
|
JGS_CT
|
10.83421657
|
1.38E-25
|
11.31
|
-
|
0
|
-
|
TRINITY_DN47054_c0_g1
|
ZY_NJ
|
10.98642411
|
2.48E-25
|
-
|
23.55
|
-
|
0
|
AAF74732.1 trypsin precursor AiT6
|
ZY_CT
|
11.10415117
|
6.86E-26
|
-
|
23.55
|
0
|
-
|
JGS_NJ
|
10.68823818
|
8.35E-24
|
18.27
|
-
|
-
|
0
|
JGS_CT
|
10.80596523
|
2.05E-24
|
18.27
|
-
|
0
|
-
|
TRINITY_DN57295_c1_g2
|
ZY_NJ
|
10.96724498
|
3.16E-25
|
-
|
39.86
|
-
|
0
|
XP_022821848.1 actin cytoskeleton-regulatory complex protein PAN1-like
|
ZY_CT
|
11.08497204
|
8.7E-26
|
-
|
39.86
|
0
|
-
|
JGS_NJ
|
10.69980682
|
7.81E-24
|
31.87
|
-
|
-
|
0
|
JGS_CT
|
10.81753387
|
1.92E-24
|
31.87
|
-
|
0
|
-
|
TRINITY_DN47254_c0_g1
|
ZY_NJ
|
10.99043276
|
8.09E-25
|
-
|
10.79
|
-
|
0
|
XP_021326591.1 vitellogenin-like
|
ZY_CT
|
11.10815982
|
2.15E-25
|
-
|
10.79
|
0
|
-
|
JGS_NJ
|
10.61636625
|
6.78E-23
|
7.69
|
-
|
-
|
0
|
JGS_CT
|
10.7340933
|
1.61E-23
|
7.69
|
-
|
0
|
-
|
TRINITY_DN57949_c0_g1
|
ZY_NJ
|
9.429327246
|
1.42E-11
|
-
|
2.38
|
-
|
0
|
XP_019817766.1 uncharacterized protein LOC109560216 isoform X1
|
ZY_CT
|
9.547054274
|
6.22E-12
|
-
|
2.38
|
0
|
-
|
JGS_NJ
|
11.7584304
|
8.97E-19
|
12.24
|
-
|
-
|
0
|
JGS_CT
|
11.87615743
|
3.32E-19
|
12.24
|
-
|
0
|
-
|
TRINITY_DN47831_c0_g1
|
ZY_NJ
|
10.27760237
|
2.64E-17
|
-
|
8.85
|
-
|
0
|
AAY43793.1 E6-4
|
ZY_CT
|
10.39532941
|
9E-18
|
-
|
8.85
|
0
|
-
|
JGS_NJ
|
11.09921467
|
1.63E-20
|
14.72
|
-
|
-
|
0
|
JGS_CT
|
11.21694171
|
5.24E-21
|
14.72
|
-
|
0
|
-
|
Within-population differences in gene expression before mating and after mating and oviposition
Because adult female spongy moth flight was found to be significantly reduced after oviposition20, we also prepared transcriptomes from RNA of virgin adult females before mating and adult females after mating and oviposition and examined differences in gene expression. Table 5 shows the number of DEGs up-regulated and down-regulated in moths before mating relative to after mating and oviposition for all four strains. Noticeably more DEGs were identified for the ESM strains compared to the ASM strains.
Table 5
The number of DEGs up-regulated and down-regulated before mating (BM) relative to after mating and oviposition (AM).
Comparisons
|
Up-regulated1
|
Down-regulated1
|
JGS_BM-AM
|
18
|
7
|
ZY_BM-AM
|
3
|
4
|
CT_BM-AM
|
128
|
23
|
NJ_BM-AM
|
592
|
21
|
1 Numbers refer to the quantity of up- or down-regulated DEGs in the before-mating (BM) sample relative to the after-mating/oviposition (AM) sample of each pairwise comparison.
No DEGs were identified that were consistently up-regulated or down-regulated in comparisons of the before-mating and after-mating and oviposition of both ASM strains. In contrast, 58 DEGs were found to be consistently up-regulated or down-regulated in these comparisons for the two ESM strains (Supplementary Table 2). All but one of these were up-regulated in the before-mating transcriptomes. Table 6 lists the single DEG which was down-regulated in ESM before-mating transcriptomes and the ten DEGs up-regulated in before-mating transcriptomes with the greatest degree of difference. The up-regulated DEGs included lysocardiolipin acyltransferase 1-like and actin muscle-type A2. One of the up-regulated DEGs in ESM comparisons was also found to be up-regulated in NJ before-mating transcriptomes (Table 5, TRINITY_DN53843_c6_g1).
Table 6
Genes that were consistently differentially expressed (DEGs) in all comparisons of ASM and ESM transcriptomes developed from moths before mating (BM) and after mating and oviposition (AM). DEGs are sorted in descending order with respect to log2-fold change, with DEGs down-regulated in before-mating ESM transcriptomes listed first, followed by DEGs up-regulated in ESM before-mating transcriptomes.
|
GEL
|
|
Gene ID
|
Comparison
|
log2FoldChange
|
Adjp
|
BM
|
AM
|
NR hits
|
TRINITY_DN55444_c2_g1
|
NJ_ BM - AM
|
-41.9624
|
2.31E-50
|
0
|
6.16
|
none
|
JGS_ BM - AM
|
-14.4299
|
0.005106
|
0
|
0.5
|
|
|
|
|
|
|
|
TRINITY_DN1848_c0_g1
|
NJ_ BM - AM
|
24.30176
|
5.84E-05
|
5.64
|
0
|
KAF9410092.1 hypothetical protein HW555_010723, partial
|
CT_ BM - AM
|
19.79454
|
0.01
|
0.19
|
0
|
TRINITY_DN43723_c1_g1
|
NJ_ BM - AM
|
9.462868
|
0.001434
|
17.64
|
0
|
XP_026734001.1 lysocardiolipin acyltransferase 1-like
|
CT_ BM - AM
|
17.25244
|
1.29E-09
|
0.11
|
0
|
TRINITY_DN52100_c0_g1
|
NJ_ BM - AM
|
10.50207
|
1.74E-05
|
7.02
|
0.03
|
CAB3223558.1 unnamed protein product
|
CT_ BM - AM
|
10.58316
|
2.39E-08
|
47.69
|
0.095
|
TRINITY_DN59230_c4_g1
|
NJ_ BM - AM
|
10.79498
|
0.000204
|
31.28
|
0.13
|
NP_001119725.1 actin, muscle-type A2
|
CT_ BM - AM
|
9.604437
|
0.000516
|
69.35
|
0.27
|
TRINITY_DN46116_c0_g1
|
NJ_ BM - AM
|
10.90386
|
6.46E-06
|
25.56
|
0.1
|
CAB3226619.1 unnamed protein product
|
CT_ BM - AM
|
7.596039
|
0.000876
|
24.06
|
0.44
|
TRINITY_DN47299_c0_g1
|
NJ_ BM - AM
|
10.29331
|
4.96E-08
|
119.68
|
0.3
|
KAG8112956.1 hypothetical protein SFRUCORN_010746
|
CT_ BM - AM
|
7.629028
|
0.000988
|
136.95
|
2.28
|
TRINITY_DN24521_c0_g1
|
NJ_ BM - AM
|
7.680281
|
0.001124
|
25.85
|
0.41
|
CAB3226695.1 unnamed protein product
|
CT_ BM - AM
|
9.814032
|
0.000842
|
9.21
|
0
|
TRINITY_DN59230_c7_g1
|
NJ_ BM - AM
|
7.093234
|
0.036808
|
123.95
|
0
|
AEB26312.1 actin
|
CT_ BM - AM
|
9.75179
|
0.001983
|
82.18
|
0
|
TRINITY_DN40225_c0_g1
|
NJ_ BM - AM
|
7.894189
|
0.001201
|
6.04
|
0.17
|
CAB3239390.1 unnamed protein product
|
CT_ BM - AM
|
7.019374
|
0.005982
|
10.56
|
0.24
|
TRINITY_DN53843_c6_g1
|
NJ_ BM - AM
|
4.759893
|
1.46E-05
|
1512.87
|
126.8
|
CAB3228006.1 unnamed protein product
|
CT_ BM - AM
|
4.407292
|
0.000516
|
780.49
|
72.87
|
JGS_ BM - AM
|
4.014438
|
0.02672
|
715.44
|
41.71
|